swfdr
This is the released version of swfdr; for the devel version, see swfdr.
Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates
Bioconductor version: Release (3.23)
This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ.
Author: Jeffrey T. Leek, Leah Jager, Simina M. Boca, Tomasz Konopka
Maintainer: Simina M. Boca <smb310 at georgetown.edu>, Jeffrey T. Leek <jtleek at gmail.com>
citation("swfdr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("swfdr")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("swfdr")| Computing covariate-adjusted q-values | R Script | |
| Tutorial for swfdr package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MultipleComparison, Software, StatisticalMethod |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.4) |
| Imports | methods, splines, stats4, stats |
| System Requirements | |
| URL | https://github.com/leekgroup/swfdr |
| Bug Reports | https://github.com/leekgroup/swfdr/issues |
See More
| Suggests | dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | swfdr_1.38.0.tar.gz |
| Windows Binary (x86_64) | swfdr_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | swfdr_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | swfdr_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/swfdr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/swfdr |
| Bioc Package Browser | https://code.bioconductor.org/browse/swfdr/ |
| Package Short Url | https://bioconductor.org/packages/swfdr/ |
| Package Downloads Report | Download Stats |